1. Proteins
Proteins are a major constituent of most cells (>50% dry weight)
They are important as structural and control elements in the cell and organism.
Proteins are made from 20 common amino acids (monomers)
Conformation of folding plus the chemistry of well-placed functional groups control a protein's function (another example of function follows form)

2. Polymers of a-amino acids are called peptides
MEMORIZE the basic structure of an amino acid: All have a Carboxyl group at one end and an amino group on the other.
The Side Chain comes off the central Carbon (symbolized “R”)

3. Coming together to make a peptide bond.
amino acid basics
Animation of Peptide Bond Formation
Animation - Amino acid condensation
The carboxyl group of one is adjacent to the amino group of the other, an enzyme can join the amino acids by dehydration reaction.

4. The 20 common α-Amino Acids
WHAT do you notice that is the SAME for all of them?
Different for all of them? Just by looking, could you group any of them together?

5. Side chains MAKE the AA!
The side chain determines characteristics of an amino acid: hydrophobic (nonpolar), hydrophilic (polar), acidic (neg chg), or basic (pos chg).

6. How Are the AA linked together?
The carboxyl group of one is adjacent to the amino group of the other, an enzyme can join the amino acids by dehydration reaction.

7. How Are the AA linked together?
Our FAVORITE reaction: Dehydration Synthesis (and Hydrolysis to break peptide bonds!)
amino acid basics (peptide Bond formation)
Animation of Peptide Bond Formation
Animation - Amino acid condensation

8. Shape is everything
In order for a protein to function properly it must be able to be recognized and fit properly to another molecule. (This is important to remember when we speak of enzymes & antibodies)

9. A proteins function depends on its conformation.
A polypeptide is not the same as a protein.
The chain of amino acids (known as a polypeptide) must be twisted and folded to become the FUNCTIONAL protein.

10. 2 types you need to know
Globular - clumped into a shape of a ball. Major examples include insulin, hemoglobin, and most enzymes.
Fibrous proteins Keratins - in wool, hair skin, fur, claws, nails, hooves, horns, scales, beaks, feathers, actin and mysin in muscle tissues and fibrinogen needed for blood clots.

11. Four levels of protein structure all driven by chemical bonds
PRIMARY Structure: The unique sequence of amino acids in a polypeptide chain. Even slight changes in primary structure can affect a protein’s confirmation and ability to function.
It is formed by peptide bonds between amino acids.
Amino terminus = AA1; Carboxyl end is LAST AA
What ULTIMATELY determines the primary structure of a Protein?

12. 2° Structure
Arrangement in space of the polypeptide backbone (the linked regions of the amino acids- amino group, carboxyl group, and central carbon)
Two basic shapes: a- helix and b-pleated sheet

13. Two types of secondary structure
Alpha - Helix: the first structure. It has a rod shape. The peptide is coiled around an imaginary cylinder and stabilized by hydrogen bonds formed between every 4th amino acid

14. The second type
Beta - pleated sheets: 2 or more regions of the polypeptide chain lie parallel to each other
Hydrogen bonds between the parts of the backbone in parallel regions hold the structure together (like a folded sheet of paper).

15. Linus Pauling
The only person to be awarded TWO Nobel Prizes in TWO different fields!
Chemistry for protein structure
Discovered alpha helix – polypeptide chain

16. Tertiary (3°) Structure
Overall shape of the protein including side chains. Most proteins are globular (roughly spherical) others are fibrous in shape

17. 3° Struc, cont.
Irregular contortions in the structure caused by interactions between side chains (R groups) of the various AA
Certain amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino acids in the same chain.
Hydrophobic interactions also contribute to the tertiary structure
Hydrogen bonds between polar side chains
Ionic bonds between pos/ neg charged side chains

18. Quaternary Structure
The overall configuration that results from the aggregation of polypeptide subunits.
An example of this is the molecule hemoglobin (with 4 subunits).

19. Protein folding
Interactive Concepts in Biochemistry - Interactive Animations
structure.swf
Proteins Structure Animation

20. Summary of Protein Structure!
1° structure- sequence of aa’s; Ultimately determines shape of the protein & thus function
2° Structure: H-bonds form α-helices and β-pleated sheets between the polypep backbone
3° Structure: interactions between side (R) groups; H-bonds, hydrophobic interactions, hydrophilic interactions, S-S bridges, ionic bonds, covalent bonds and acid/base interactions all contribute
4° Structure: 2 or more polypeptide chains aggregated into one functional macromolecule.

21. What else does protein conformation depend on?
pH, salt concentration, temperature or other aspects of the environment are altered, the protein may unravel and LOSE its native conformation (DENATURE)
Denatured proteins are almost always inactive
When conditions return to normal, the protein may or may not renature & be active again.

22. Several function of proteins.
Structural proteins act as support. Examples include the silk fibers (β pleated sheets!) of spiders and insects, collagen in animal connective tissue, and keratin (α helix!) found in hair, horns, feathers.

23. Storage proteins
Storage of amino acids. Examples are egg whites, casein, found in milk, and plants have storage proteins in their seeds.

24. Transport proteins Transport of other substances.
Hemoglobin is an example, transporting oxygen from the lungs to other parts of the body. McGraw-Hill Online Learning Center Test<BLURT>

25. Hormonal (Signal) Proteins
They perform by coordinating an organism's activities. An example is insulin.

26. Receptor (Sensory) proteins
Receive a signal and tell cell to respond to the stimulus.
Receptors built into the membrane of nerve cells detect chemical signals released by other nerve cells.

27. Contractile Proteins
Used for movement. Examples are actin and myosin found in muscle tissue.

28. Defensive Proteins
Protection from disease. Antibodies are an exampe.

29. Enzymatic Proteins
Selective acceleration of chemical reactions. We will be discussing enzymes in detail later.

30. Chaperone Proteins
Scientists have discovered chaperone proteins, molecules that function as temporary braces to assist with proper folding Biology I Interactive Animations (go to life cycle of protein)

31. Name the Different types of proteins in this image!31

32. Tutorial 3.2 Macromolecules ( go to proteins )